US10968460B2 - High temperature seed germination - Google Patents

High temperature seed germination Download PDF

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US10968460B2
US10968460B2 US15/451,497 US201715451497A US10968460B2 US 10968460 B2 US10968460 B2 US 10968460B2 US 201715451497 A US201715451497 A US 201715451497A US 10968460 B2 US10968460 B2 US 10968460B2
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nxs
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US20170183682A1 (en
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Eric Roland Coppoolse
Miriam POST
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Rijk Zwaan Zaadteelt en Zaadhandel BV
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8262—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield involving plant development
    • C12N15/8267—Seed dormancy, germination or sprouting
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/90—Isomerases (5.)
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H5/00—Angiosperms, i.e. flowering plants, characterised by their plant parts; Angiosperms characterised otherwise than by their botanic taxonomy
    • A01H5/12—Leaves
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y503/00—Intramolecular oxidoreductases (5.3)
    • C12Y503/99—Other intramolecular oxidoreductases (5.3.99)
    • C12Y503/99009—Neoxanthin synthase (5.3.99.9)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the present invention relates to a seed that is capable of germinating at a high temperature.
  • the invention further relates to plants, progeny and propagation material that produce seeds with this capacity and their uses.
  • the invention relates in particular to high temperature germination in lettuce.
  • thermoinhibition a mechanism known as secondary or induced dormancy, to prevent premature seed germination during supraoptimal temperatures, such as those that may occur during hot summer months.
  • ABA phytohormone abscisic acid
  • Seed priming allows for the controlled hydration of seeds, allowing the seeds to complete the first steps in the germination process before they are dried back to their original moisture content, and stored until planting.
  • One of the primary benefits of seed priming is the ability to alleviate thermoinhibition by increasing the maximum temperature at which germination will occur.
  • seed priming may be beneficial to seed germination, it is an expensive procedure in terms of labour and equipment requirements, the types of ingredients that are used, and the time it requires for hydrating and drying back the seeds.
  • the priming process may result in a reduction of the shelf life of primed seeds, as compared to untreated seeds. This undesirable side effect is influenced by the rate and extent of the drying back procedure.
  • Improving the capability of seeds to germinate at a high temperature may also enlarge the total acreage for vegetable cultivation. Areas of the world with relatively warm winters are currently unsuitable for certain crops to grow, since the germination capabilities of such varieties may be insufficient to overcome thermoinhibition under such high temperatures.
  • NXS neoxanthin synthase
  • NXS is an enzyme in the ABA pathway which catalyses the formation of neoxanthin from violaxanthin, precursors of ABA.
  • NXS is an enzyme in the ABA pathway
  • modifications to the NXS gene and/or encoded NXS protein that will lead to a lower neoxanthin level will also lead to a reduction in ABA levels, thus allowing for seed germination to still occur at high temperatures.
  • the highly conserved nature of the ABA pathway means that modifications to the NXS gene and the resultant trait, like those which were found in the present research, are widely applicable to other plant species in which an orthologous NXS gene with a similar function exists.
  • FIGS. 1A-C Lettuce ( Lactuca sativa ) NXS (genomic) DNA (SEQ ID No. 1; FIGS. 1A-1B ) and NXS protein sequence (SEQ ID No. 2; FIG. 1C ).
  • the ATG translation start site is bolded and underlined.
  • the wild type positions of the two modified codons (T 3017 G 3018 G 3019 and C 3518 C 3519 A 3520 ) and conserved tryptophan codon (T 3196 G 3197 G 3198 ) are in bold and underlined.
  • FIGS. 1A-C in the priority applications and all references to FIGS. 1A-C therein began at and included the ATG translation start site which is located downstream from the first nucleotide in the figure.
  • the numbering of SEQ ID No:1 in the current application and all references to SEQ ID No:1 herein begins at the first nucleotide position that is shown in the figure, which is upstream of the start codon.
  • the following Table indicates nucleotide positions as they were numbered in the priority application(s) in relation to the ATG start codon and their corresponding numbering in SEQ ID NO:1 of the current application.
  • FIG. 2A-2GG DNA sequence of NXS orthologues.
  • FIG. 2A ; 2 B Daucus carota (variant 1 and 2),
  • FIG. 2C Cichorium endivia
  • FIGS. 2D ; 2 E and 2 F Solanum melongena (variant 1 and 2),
  • FIG. 2M Brassica oleracea
  • FIG. 2N ; 2 O Apium graveolens (variant 1 and 2),
  • FIG. 2P Spinacia oleracea
  • FIG. 2Q Valerianella locusta
  • FIG. 2R Rhaphanus sativus
  • FIG. 2S Capsicum baccatum
  • FIG. 2T Chenopodium quinoa
  • FIG. 2U Fagopyrum esculentum
  • FIG. 2V Lens esculenta
  • FIG. 2Y Pisum sativum
  • FIG. 2DD Chicorium intybus
  • FIGS. 3A-3F Protein sequence of NXS orthologues Daucus carota (variant 1 and 2), Cichorium endivia, Solanum melongena (variant 1 and 2), Solanum lycopersicum (variant 1 and 2), Capsicum annuum, Brassica oleracea, Apium graveolens (variant 1 and 2), Spinacia oleracea, Valerianella locusta, Rhaphanus sativus, Capsicum baccatum, Chenopodium quinoa, Fagopyrum esculentum, Lens esculenta, Medicago sativa, Pisum sativum, Vigna radiata (variant 1 and 2), Trigonella foenum - graecum, Chicorium intybus, Allium cepa (variant 1 and 2), Hordeum vulgare.
  • FIGS. 4A-4C Multiple sequence alignment of orthologous NXS protein sequences from plant species from FIGS. 3A-3F and Table 1.
  • FIGS. 4A-4C disclose SEQ ID NOS 39, 40, 30, 31, 38, 43, 57, 37, 44, 35, 36, 33, 34, 45, 41, 46, 42, 58-61, 47, 48, 62, 49-52, 32, 53, 2, 63, 54-56 and 64-69, respectively, in order of appearance.
  • FIG. 5A Graph showing the final germination percentages over a given temperature range, for the wild type Sensa ⁇ seed lot and Ls_mt_sen mutant seed lot.
  • the GT50 Dark is the temperature at which the final germination percentage is expected to be 50%.
  • FIG. 5B Graph showing the final germination percentages over a given temperature range, for the wild type Burovia seed lot and Ls_mt_bur mutant seed lot.
  • the GT50 Dark is the temperature at which the final germination percentage is expected to be 50%.
  • FIG. 5C Graph showing the final germination percentages over a given temperature range, for both wild type seed lots of Sensa ⁇ and Burovia and mutant seed lots.
  • the GT50 Dark is the temperature at which the final germination percentage is expected to be 50%.
  • the present invention thus provides seeds which may comprise a modified NXS gene and/or modified regulatory sequences thereof in its genome.
  • the invention relates to seed which may comprise in its genome a modified NXS gene and/or modified regulatory sequences thereof, wherein the modified NXS gene and/or modified regulatory sequences thereof provides the seed with the capability to germinate at a high temperature as compared to wild type seed not having the modified NXS gene and/or modified regulatory sequences thereof.
  • the invention relates to a modified NXS gene and/or modified regulatory sequences thereof which provides a seed with the capability to germinate at a high temperature as compared to a wild type seed not having the modified NXS gene and/or modified regulatory sequences thereof in its genome.
  • the trait of the invention is the phenotype in which a seed which may comprise a modified NXS gene and/or modified regulatory sequences thereof in its genome has the capability to germinate at a high temperature. More in particular, in one embodiment the invention is the phenotype in which a seed which may comprise a modified NXS gene and/or modified regulatory sequences thereof in its genome has the capability to germinate at a high temperature in the dark. “Trait of the invention”, “trait”, or “phenotypic trait”, may be used interchangeably.
  • the invention relates to a modified Lactuca sativa NXS gene, the wild type of which is identified in SEQ ID No. 1, encoding the protein of SEQ ID No. 2.
  • the invention relates to lettuce ( Lactuca sativa ) seed which may comprise in its genome a modified NXS gene, wherein the modified NXS gene provides the seed in an unprimed state with the capability to germinate at a high temperature as compared to wild type seed not having the modified NXS gene.
  • the modification can also relate to the regulatory sequences of the gene.
  • regulatory sequences can be enhancer sequences that are located within the intronic regions of the gene or may be located upstream or downstream of the gene that it regulates. Such regulatory sequences may even be located far removed from the gene on another part of the chromosome or even on another chromosome. Regulatory sequences thus control or regulate gene expression.
  • the said capability to germinate at a high temperature is controlled by modifications to the NXS gene and/or regulatory sequences thereof, the inheritance of which are consistent with that of a monogenic recessive trait.
  • the term “recessive trait” is to mean in the context of this application that the fully achievable trait is only observable in seeds of a plant which may comprise a modified NXS gene and/or modified regulatory sequences thereof in the homozygous state. Since the inheritance of the trait is comparable to that of a monogenic trait, it is advantageous in that the trait can easily be incorporated into various plant types for a given plant species.
  • modification refers to changes to the wild type NXS gene and/or wild type regulatory sequences thereof that lead to a “modified” version of the wild type gene.
  • a “gene” in the context of this application may comprise exonic sequences and regulatory sequences such as a promoter sequence and if present also may comprise intronic sequences. Modifications to the NXS gene and/or regulatory sequences thereof, may inhibit gene transcription such that the expression of the modified gene is reduced or prevented. Modifications may also be changes to the sequence of the NXS gene and/or regulatory sequences thereof that lead to a reduced level, reduced activity or complete absence of the encoded NXS protein.
  • the invention also relates to an NXS gene which may comprise a modification in its coding sequence and/or its regulatory sequences and/or splice sites as compared to the wild type sequence, wherein the modification results in an increase in the germination temperature of the seed which may comprise the modified gene in its genome.
  • coding sequence is the portion of the gene's DNA composed of exons that code for protein.
  • splice site is a recognition site at which splicing of an intron takes place during the processing of pre-mRNA into mature mRNA. Splice sites are found at the 5′ and 3′ ends of introns. Splice sites are also intended to fall under the more general term “regulatory sequences”.
  • the invention relates to a lettuce NXS gene which may comprise a modification in its coding sequence and/or its regulatory sequences and/or splice sites as compared to the wild type sequence of SEQ ID No. 1, wherein the modification results in an increase in the germination temperature of the seed which may comprise the modified gene.
  • wild type refers to the form of an organism, strain, gene, characteristic or trait as it would occur in nature, and is in contrast to the mutated form for example.
  • seed germination is strongly temperature dependent. Within a batch of seeds every single seed may or may not germinate at a particular temperature. Preferably all seeds or at least a high percentage of the seeds germinate at an optimum germination temperature range. If the temperature increases above the optimum germination temperature range, the germination percentage of a batch of seeds declines sharply.
  • the germination temperature of a seed lot can be measured in terms of the “Germination Temperature 50” (GT50), which is the temperature at which 50% of the seeds of a given seed lot will germinate. When seeds of a given seed lot are exposed to temperatures above the GT50, they may become thermodormant or die. The GT50 may differ amongst different cultivars within a given crop.
  • seed lot as used in this application is to mean, a batch of seeds produced from a mother plant.
  • a seed lot consists preferably of a minimum of 100 seeds. When less than 100 seeds are used to determine the GT50 of a seed lot, the GT50 becomes less accurate.
  • Seed lots which may comprise seeds having a modified NXS gene, as well as their corresponding wild type seed lots, should be produced in the same production environment to be comparable.
  • the skilled person is familiar with the production environment for different plant species.
  • lettuce seed lots in the context of the invention i.e. with the GT50 values described herein, were produced at a latitude of 52°, in an Oceanic climate having a Köppen-classification of Cfb (McKnight & Hess, 2000. Physical Geography: A Landscape Appreciation. Upper Saddle River, N.J.: Prentice Hall).
  • the upper temperature cut-off point “GT50 Dark”, as used in this application is to mean, the temperature at which 50% of the seeds of a given seed lot will germinate when sown on paper in the dark.
  • the GT50 Dark is measured under continuous dark conditions (24 h/day) as this mimics germination conditions when seeds are planted beneath the soil or when seeds are encapsulated in pellets. Exposure of seeds belonging to the seed lot above the GT50 Dark, may cause the seeds to become thermodormant or die.
  • the skilled person is able to determine the GT50 Dark of a seed lot using a two step method. Firstly, germination tests are performed at different temperatures, in order to determine the cumulative germination percentage over time at a given temperature. For each seed lot to be tested, preferably 100 seeds are sown on top of a round filter paper wetted with tap water. These are in turn placed inside of a non-transparent plastic tray, which itself is lined with a large square piece of beet filter paper also wetted with tap water. A temperature recording device is placed on the beet filter paper to record the actual germination temperature at seed level. The tray is then closed with a well-fitted non-transparent lid, and placed inside a dark plastic bag. The tray is then placed inside a pre-heated incubator at the desired temperature. Biological replicates are preferably sown in different trays and at different points of time to remove any biases related to sowing.
  • thermostable room which is closed from all outside light sources. Additionally, the thermostable room is lit with for example, with green safe lights (Philips TL-D 36 W/17 Green) to prevent any light effects on germination.
  • germination is preferably scored twice a day. As used herein, “germination” occurs when radical protrusion is visible. Germinated seeds are counted and then removed at every counting moment. If there are dead or dormant seeds in the seed lot being tested, germination is followed for at least four extra counting moments until no additional germination is observed. The final germination percentage of a given seed lot, at a given temperature, can then be determined by plotting a “Germination over Time” curve. The final germination percentage is calculated as the number of germinated seeds at the end of scoring/the number of seeds sown for testing ⁇ 100%.
  • the final germination percentage is 100%.
  • the “final germination percentage” is the percentage of germination of a seed lot, after which no more germination occurs.
  • the final germination percentage from each “Germination over Time” curve is then plotted per actual measured temperature, for example in the case of lettuce from 18° C. to 42° C. ( FIGS. 5A, 5B and 5C ).
  • a line of best fit is used for example, to fit the final germination percentages into a curve for each seed lot. The skilled person is familiar with this practice.
  • the GT50 Dark can be determined per seed lot.
  • the GT50 Dark corresponds to the temperature at which the final germination percentage is expected to be 50%.
  • seeds of a given seed lot are exposed to temperatures above the GT50 Dark, they may become thermodormant or die.
  • the invention relates to a seed lot wherein the seeds belonging to the seed lot may comprise a modified NXS gene and/or modified regulatory sequences, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature, and which seed lot is characterized in that the GT50 Dark of said seed lot is at least 5° C. higher than the GT50 Dark of a seed lot of seeds not comprising the modified NXS gene and/or modified regulatory sequences thereof.
  • the invention relates to a seed which may comprise in its genome a modified NXS gene and/or modified regulatory sequences, wherein said seed belongs to a seed lot having a GT50 Dark that is at least 5° C. higher than the GT50 Dark of a seed lot which may comprise seeds not having the modified NXS gene and/or modified regulatory sequences thereof.
  • the GT50 Dark of a seed lot of seeds having a modified NXS gene and/or modified regulatory sequences thereof or the germination temperature of the seed having a modified NXS gene and/or modified regulatory sequences thereof is between 5° C. and 25° C., between 6° C. and 25° C., between 7° C. and 25° C., between 8° C. and 25° C., between 9° C. and 25° C., between 10° C. and 25° C., between 11° C. and 25° C., between 12° C. and 25° C., between 13° C. and 25° C., between 14° C. and 25° C., between 15° C. and 25° C., between 16° C. and 25° C., between 17° C.
  • the said seed may comprise a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present, provides the seed with the capability to germinate at a high temperature, in particular at a temperature of at least 20° C.
  • the GT50 Dark of the seed lot or the germination temperature of the seed lies between 20° C. and 40° C., between 21° C. and 40° C., between 22° C. and 40° C., between 23° C. and 40° C., between 24° C. and 40° C., between 25° C. and 40° C., between 26° C. and 40° C., between 27° C. and 40° C., between 28° C. and 40° C., between 29° C. and 40° C., between 30° C. and 40° C., between 31° C. and 40° C., between 32° C. and 40° C., between 33° C. and 40° C., between 34° C. and 40° C., between 35° C. and 40° C., between 36° C. and 40° C., between 37° C. and 40° C., between 38° C. and 40° C., between 39° C. and 40° C.
  • 40° C. is the maximal biological temperature allowable for seed germination. This also means that the increase in GT50 Dark of a seed lot of seeds or the germination temperature of the seed which is provided by having a modified NXS gene and/or modified regulatory sequences thereof homozygously present in the genome of said seeds, will not provide said seeds with the capability to germinate beyond the biological maximum of 40° C., regardless of the relative increase provided by the modified NXS gene.
  • the GT50 Dark of a seed lot of seeds which may comprise a modified NXS gene and/or modified regulatory sequences thereof or the germination temperature of the seed which may comprise a modified NXS gene and/or modified regulatory sequences thereof may be lower than temperatures of at least 20° C.
  • the GT50 Dark of a seed lot of seeds having a modified NXS gene and/or modified regulatory sequences thereof or the germination temperature of the seed having a modified NXS gene and/or modified regulatory sequences thereof is still between 5° C. and 25° C., between 6° C. and 25° C., between 7° C.
  • the invention relates to a plant which may comprise a modified NXS gene and/or modified regulatory sequences thereof in its genome, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature.
  • the high temperature is as defined above.
  • the invention relates to a seed lot of the species Lactuca sativa wherein the seeds belonging to the seed lot may comprise a modified NXS gene, which when homozygously present in a seed, provides the seeds in an unprimed state with the capability to germinate at a high temperature, and which seed lot is characterized in that the GT50 Dark of said seed lot is at least 10° C. higher than the GT50 Dark of a seed lot of seeds not comprising the modified NXS gene.
  • the invention relates to a Lactuca sativa seed which may comprise in its genome a modified NXS gene, wherein said seed belongs to a seed lot having a GT50 Dark that is at least 10° C. higher than the GT50 Dark of a seed lot which may comprise seeds not having the modified NXS gene.
  • the GT50 Dark of a seed lot of seeds of the species Lactuca sativa having a modified NXS gene or the germination temperature of the seed having a modified NXS gene is between 10° C. and 25° C., between 11° C. and 25° C., between 12° C. and 25° C., between 13° C. and 25° C., between 14° C. and 25° C., between 15° C. and 25° C., between 16° C. and 25° C., between 17° C. and 25° C., between 18° C. and 25° C., between 19° C. and 25° C., between 20° C. and 25° C., between 21° C. and 25° C., between 22° C.
  • the said Lactuca sativa seed may comprise a modified NXS gene, which when homozygously present, provides the seed in an unprimed state with the capability to germinate at a high temperature, in particular at a temperature of at least 31.8° C.
  • the GT50 Dark of the seed lot or the germination temperature of the seed lies between 28° C. and 40° C., between 31.8° C. and 40° C., between 32° C. and 40° C., between 33° C. and 40° C., between 34° C. and 40° C., between 35° C. and 40° C., between 36° C. and 40° C., between 37° C. and 40° C., between 38° C. and 40° C., between 39° C. and 40° C.
  • the invention relates to a lettuce plant ( Lactuca sativa ) which may comprise a modified NXS gene, which when homozygously present in a seed, provides the seed in an unprimed state with the capability to germinate at a high temperature.
  • the high temperature is as defined above.
  • Modifying the NXS gene and/or modified regulatory sequences thereof may lead to changes in the expression of the gene.
  • the invention relates to seed which may comprise in its genome a modified NXS gene and/or modified regulatory sequences thereof, wherein the expression of the modified NXS gene is substantially reduced or prevented and this reduction or prevention causes the seed to be able to germinate at a higher temperature than the wild type seed not comprising a modified NXS gene and/or modified regulatory sequences thereof.
  • the invention relates to seed which may comprise in its genome a modified NXS gene and/or modified regulatory sequences thereof, wherein the expression of the modified NXS gene is reduced or prevented.
  • the invention relates to a modified NXS gene and/or modified regulatory sequences thereof wherein the expression of said gene when present in the genome of a seed or plant is substantially reduced or prevented. In another embodiment, the invention relates to a modified NXS gene and/or modified regulatory sequences thereof wherein the expression of said gene is reduced or prevented.
  • the expression of the NXS gene is reduced or prevented in the context of this invention, this is to mean that the expression of the modified NXS gene is less than the expression of the wild type NXS gene or is prevented and thus absent.
  • the said reduction or prevention of gene expression is directly or indirectly responsible for the trait of high temperature germination of the invention.
  • the invention relates to lettuce ( Lactuca sativa ) seed which may comprise in its genome a modified NXS gene, wherein the expression of the modified NXS gene is substantially reduced or prevented.
  • gene expression may be reduced or prevented by means of preventing the transcription of the gene.
  • Preventing transcription may for example be achieved by means of RNA oligonucleotides, DNA oligonucleotides or RNAi molecules directed against the NXS gene promoter, or preferably by means of the expression of a negatively acting transcription factor acting on the NXS gene promoter.
  • Gene expression may also be reduced or prevented by destabilizing NXS mRNA or transcript, preferably by means of nucleic acid molecules that are complementary to the NXS mRNA or transcript, selected from the group consisting of antisense RNA, RNAi molecules, Virus-Induced Gene Silencing (VIGS) molecules, co-suppressor molecules, RNA oligonucleotides or DNA oligonucleotides.
  • destabilizing mRNA or transcripts are well known to the person skilled in the art.
  • the invention relates to seed having a reduced level, reduced activity or complete absence of NXS protein.
  • the invention relates to seed having a reduced level, reduced activity or complete absence of NXS protein, resulting from a modification of the NXS gene and/or modified regulatory sequences thereof which encodes it.
  • the invention relates to a modified NXS gene and/or modified regulatory sequences thereof, characterized in that seed which may comprise said modified gene and/or modified regulatory sequences thereof have a reduced level, reduced activity or complete absence of the encoded NXS protein.
  • a reduced level or complete absence of the NXS protein may occur by disrupting the transcription of the NXS gene, for example by introducing one or more mutations in the NXS gene promoter sequence.
  • a reduced activity of the NXS protein may occur for example by introducing one or more mutations into the coding sequence of the NXS gene. Mutation(s) to the NXS gene may affect the biological function of the encoded protein, as compared to NXS protein encoded by a wild type NXS gene where no such mutation(s) is present.
  • the invention relates to lettuce ( Lactuca sativa ) seed having a reduced level, reduced activity or complete absence of NXS protein.
  • lettuce seeds that germinate at a high temperature were identified to comprise a mutation in the NXS gene.
  • One of the identified mutations led to a premature stop codon in the coding sequence of the lettuce NXS gene ( FIGS. 1A-B , SEQ ID No. 1).
  • Another mutation led to an amino acid substitution in a highly conserved residue of the lettuce NXS protein ( FIG. 1C , SEQ ID No. 2).
  • the invention relates to lettuce seed which may comprise in its genome a modified NXS gene, wherein the modified NXS gene may comprise a premature stop codon.
  • the invention relates to lettuce seed which may comprise in its genome a modified NXS gene, wherein the modified NXS gene encodes an NXS protein that may comprise one or more amino acid substitutions.
  • Both types of mutations provided the respective mutant lettuce seeds with the ability to germinate at a high temperature, which is well above the germination temperature for the corresponding wild type lettuce seeds (see Examples 1-3 and FIG. 5A, 5B, 5C ). It was found that the modification to the NXS gene wherein a conserved proline residue is substituted with a serine residue, provided the seeds with a significantly higher capability to germinate at a high temperature as compared to the wild type seed. The modification to the NXS gene wherein a premature stop codon is introduced also increases the germination temperature (see Table 2 of Example 3B showing the relative increase in GT50 Dark between mutant seed lots and wild type seed lots, and Example 4).
  • the invention relates to seed which may comprise in its genome a modified NXS gene, wherein the modified NXS gene may comprise a premature stop codon.
  • the invention relates to a modified NXS gene wherein said gene may comprise a premature stop codon.
  • the invention relates to lettuce seed having a modified NXS gene, wherein the modification is a premature stop codon located within exon 3, exon 4, or exon 5 of the lettuce NXS gene according to SEQ ID No. 1. More in particular, the premature stop codon is the result of a mutation of residue G 3018 >A 3018 of the lettuce NXS gene according to SEQ ID No. 1.
  • the invention relates to seed which may comprise in its genome a modified NXS gene, wherein the modified NXS gene encodes an NXS protein that may comprise one or more amino acid substitutions.
  • the invention relates to a modified NXS gene wherein said gene encodes an NXS protein that may comprise one or more amino acid substitutions.
  • Mutation(s) in the NXS gene and/or regulatory sequences thereof are preferably introduced randomly by means of one or more chemical compounds, such as ethyl methane sulphonate (EMS), nitrosomethylurea, hydroxylamine, proflavine, N-methly-N-nitrosoguanidine, N-ethyl-N-nitrosourea, N-methyl-N-nitro-nitrosoguanidine, diethyl sulphate, ethylene imine, sodium azide, formaline, urethane, phenol and ethylene oxide, and/or by physical means, such as UV-irradiation, fast neutron exposure, X-rays, gamma irradiation, and/or by insertion of genetic elements, such as transposons, T-DNA, retroviral elements.
  • chemical compounds such as ethyl methane sulphonate (EMS), nitrosomethylurea, hydroxylamine, proflavine, N-methly-N-nitro
  • Mutagenesis also may comprise the more specific, targeted introduction of at least one modification by means of homologous recombination, oligonucleotide-based mutation introduction, zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs) or Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) systems.
  • ZFN zinc-finger nucleases
  • TALENs transcription activator-like effector nucleases
  • CRISPR Clustered Regularly Interspaced Short Palindromic Repeat
  • mutations that may lead to a reduced activity of the NXS protein are mutations to the NXS coding sequence that give rise to premature stop codons, frame shifts or amino acid changes in the encoded protein. Premature stop codons typically lead to the expression of a truncated version of the encoded protein.
  • a truncated version of a protein may lack one or more domains that are essential to perform its function and/or to interact with substrates or with other proteins, and/or it may lack the ability to fold properly into a functional protein.
  • Frame shift mutations are caused by the introduction or deletion of one or more base pairs in a DNA sequence encoding a protein.
  • the triplet codon encoding the individual amino acids of the protein sequence become shifted relative to the original open-reading frame, and the encoded protein sequence changes dramatically.
  • Protein translation will result in an entirely different amino acid sequence than that of the originally encoded protein, and often a frame shift also leads to a premature stop codon in the open reading frame. The overall result is that the encoded protein no longer has the same biological function as the originally encoded protein.
  • Amino acid changes in an encoded protein sequence arise when the mutation of one or more base pairs in the coding sequence results in an altered triplet codon, encoding a different amino acid. Due to the redundancy of the genetic code not all point mutations lead to amino acid changes. Such mutations are termed “silent mutations”. Some amino acid changes are “conservative”, i.e. they lead to the replacement of one amino acid by another amino acid with comparable properties, such that the mutation is unlikely to dramatically change the folding of the mature protein, or influence its function.
  • amino acid changes are non-silent, non-conservative amino acid changes in domains that play a role in substrate-recognition, the active site of enzymes, interaction domains or in major structural domains (such as transmembrane helices) may partly or completely destroy the functionality of an encoded protein, without thereby necessarily affecting the expression level of the encoding gene.
  • a “non-conservative amino acid change” occurs when one amino acid is replaced by another amino acid with different chemical properties, which may lead to detrimental stability, functionality and/or structural effects of the encoded protein.
  • Mutations in the promoter sequence of the NXS gene may also perturb the biological function of the encoded NXS protein, as such mutations may lead to a complete lack of transcription of the gene (e.g. subsequently resulting in a complete absence of the NXS protein), or to a significantly decreased and biologically inadequate level of transcription (e.g. subsequently resulting in a reduced level of the NXS protein).
  • Mutations in splice sites may also perturb the biological function of the encoded protein, because if a splice site is destroyed by a mutation, the amino acid sequence encoded in the mature mRNA transcribed from the gene will not be correct, and it may easily contain frame shifts and/or premature stop codons. In either case, the protein sequence translated from such an mRNA will not be identical to the originally encoded protein sequence, which will most likely have serious consequences for the biological functionality of the translated protein.
  • amino acid substitutions produce a conservative change and result in a functionally equivalent protein.
  • Conservative amino acid substitutions may be made on the basis of chemical properties, for example similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity or the amphipathic nature of the residues, in which case the resulting protein may still function normally.
  • the amino acid substitution may occur in a region of the protein that does not significantly affect the protein structure or function.
  • an amino acid substitution that occurs at a well conserved or invariant position that is essential for the structure and/or function of the protein, or substitutions with amino acids that do not share conserved chemical properties may lead to non-conservative amino acid changes.
  • the invention relates to seed which may comprise in its genome a modified NXS gene, wherein the modified NXS gene may comprise a premature stop codon and/or encodes an NXS protein that may comprise one or more amino acid substitutions.
  • the invention relates to a modified NXS gene wherein said gene may comprise a premature stop codon and/or encodes an NXS protein that may comprise one or more amino acid substitutions.
  • the invention relates to seed which may comprise in its genome a modified NXS gene, wherein a conserved residue of the encoded NXS protein is substituted.
  • the invention relates to a modified NXS gene wherein said gene encodes a NXS protein in which a conserved residue is substituted. Mutations in the NXS gene leading to non-conservative amino acid changes at these conserved positions in the encoded protein, lead to a reduced level, reduced activity or complete absence of NXS protein.
  • the conserved residue is in particular a proline residue which was found to be very highly conserved in a multiple sequence alignment of the NXS protein of more than 200 unrelated species (results not shown).
  • this conserved proline is substituted with a serine residue, or any other non-conservative amino acid change which would disrupt the stability, functionality, and/or structure of the encoded NXS protein.
  • the skilled person is familiar with substitutions which would be non-conservative amino acid changes for a given amino acid.
  • the invention relates to a modified lettuce NXS gene, wherein a highly conserved proline residue at position 212 in the lettuce NXS protein (SEQ ID No. 2) which is encoded by C 3518 C 3519 A 3520 of the lettuce NXS DNA sequence (SEQ ID No. 1) is substituted with a serine residue (C 3518 C 3519 A 3520 >T 3518 C 3519 A 3520 ).
  • SEQ ID No. 2 a highly conserved proline residue at position 212 in the lettuce NXS protein
  • SEQ ID No. 1 which is encoded by C 3518 C 3519 A 3520 of the lettuce NXS DNA sequence (SEQ ID No. 1) is substituted with a serine residue (C 3518 C 3519 A 3520 >T 3518 C 3519 A 3520 ).
  • the conserved residue is in particular a tryptophan residue which was found to be very highly conserved in a multiple sequence alignment of the NXS protein of more than 200 unrelated species (results not shown).
  • the conserved tryptophan is located at position 175 in the lettuce NXS protein (SEQ ID No. 2) which is encoded by T 3196 G 3197 G 3198 of the lettuce NXS DNA sequence (SEQ ID No. 1).
  • this conserved tryptophan is substituted with any other non-conservative amino acid change which would disrupt the stability, functionality, and/or structure of the encoded NXS protein.
  • a seed of the invention is also a seed in which an orthologous NXS gene and/or regulatory sequences thereof is suitably modified, wherein the modified NXS gene and/or modified regulatory sequences thereof provides the seed with the capability to germinate at a high temperature, for example a seed selected from any of the species Lactuca sativa, Cichorium endivia, Cichorium intybus, Solanum melongena, Solanum lycopersicum, Capsicum annuum, Capsicum baccatum, Brassica oleracea, Apium graveolens, Spinacia oleracea, Valerianella locusta, Daucus carota, Glycine max, Rhaphanus sativus, Chenopodium quinoa, Vigna radiata, Medicago sativa, Cicer arietinum, Fagopyrum esculentum, Trigonella foenum - graecum, Allium cepa, Lens esculenta, Oryza
  • the invention further relates to a plant which may comprise in its genome a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature as compared to wild type seed not having the modified NXS gene and/or modified regulatory sequences thereof in homozygous form.
  • the modification(s) to the NXS gene and/or encoded protein results in a substantial reduction or prevention of gene expression and/or reduced activity or complete absence of NXS protein, as described above for the seed of the invention which may comprise a modified NXS gene.
  • a plant of the invention is a plant that is grown from seed exhibiting the trait of the invention, or a plant that produces seeds exhibiting the trait of the invention.
  • both parents of the seeds should have a modified NXS gene and/or modified regulatory sequences thereof.
  • a plant of the invention is also a plant in which an orthologous NXS gene and/or regulatory sequences thereof is suitably modified, which modification when present in a seed, provides the seed with the capability to germinate at a high temperature, for example a plant selected from any of the species Lactuca sativa, Cichorium endivia, Cichorium intybus, Solanum melongena, Solanum lycopersicum, Capsicum annuum, Capsicum baccatum, Brassica oleracea, Apium graveolens, Spinacia oleracea, Valerianella locusta, Daucus carota, Glycine max, Rhaphanus sativus, Chenopodium quinoa, Vigna radiata, Medicago sativa, Cicer arietinum, Fagopyrum esculentum, Trigonella foenum - graecum, Allium cepa, Lens esculenta, Oryza sativa, Zea
  • the plant of the invention is a lettuce plant ( Lactuca sativa ) which may comprise in its genome a modified NXS gene, which when homozygously present in an unprimed seed, provides the seed with the capability to germinate at a high temperature as compared to wild type seed not having the modified NXS gene.
  • a modified NXS gene and/or modified regulatory sequences thereof can be introgressed from a plant which may comprise the modified NXS gene and/or modified regulatory sequences thereof into a plant lacking the modified NXS gene and/or modified regulatory sequences thereof but having other desired traits, using crossing when the plants are sexually compatible, optionally combined with techniques that aid the development of viable seeds or facilitate development into a plant.
  • the desired traits of the plant lacking the modified NXS gene and/or modified regulatory sequences thereof can be selected from, but are not limited to, the following group: resistance to bacterial, fungal, or viral diseases, insect or pest resistance, plant size, plant type, improved shelf-life, water stress, heat tolerance, parthenocarpy and sterility.
  • a modified lettuce NXS gene can be introgressed from a Lactuca sativa plant which may comprise the modified lettuce NXS gene into a Lactuca sativa plant lacking the modified lettuce NXS gene and/or modified regulatory sequences thereof using standard breeding techniques.
  • Selection for plants that have obtained the high germination trait of the invention from a plant which may comprise the modified NXS gene and/or modified regulatory sequences thereof is started in the F1 or any further generation from a cross between the obtaining plant and a source plant by using a molecular marker that is based upon the modification to the NXS gene and/or modified regulatory sequences thereof that underlies the trait.
  • a molecular marker that is based upon the modification to the NXS gene and/or modified regulatory sequences thereof that underlies the trait.
  • suitable molecular markers are the SNP C 3518 >T 3518 and the SNP G 3018 >A 3018 in the NXS gene of lettuce ( Lactuca sativa ) according to SEQ ID No. 1.
  • selection for the modified NXS gene and/or modified regulatory sequences thereof is started in the F2 of a cross or alternatively of a backcross.
  • Selection of plants in the F2 can also be done phenotypically based on germination tests performed on the F3 seed lots, as well as by using a molecular marker(s) which directly or indirectly detect(s) the modification of the NXS gene and/or modified regulatory sequences thereof that underlies the trait.
  • Selection for plants having the modified NXS gene which when homozygously present in a seed provides the seed with the capability to germinate at a high temperature, can also be started in the F3 or a later generation.
  • Crossing can optionally be followed by embryo rescue techniques or other techniques that result in a successful combination and introgression, which techniques are known to the person skilled in the art.
  • the invention further relates to progeny of a plant which may comprise a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature.
  • progeny can be produced by sexual or vegetative reproduction of a plant of the invention or a progeny plant thereof.
  • the progeny carries the modified NXS gene and/or modified regulatory sequences thereof that causes the trait of the invention.
  • the seed When the modified NXS gene and/or modified regulatory sequences thereof is homozygously present in a seed of the progeny plant, the seed has the capability to germinate at a high temperature in the same way as or in a way similar to a seed of the plant of the invention.
  • progeny is intended to mean the offspring or the first and all further descendants from a cross with a plant of the invention that shows the trait of the invention and/or carries the modified NXS gene and/or modified regulatory sequences thereof underlying the trait.
  • the invention relates to plants that carry the trait of the invention and that have acquired the said trait by introduction of the modified NXS gene and/or modified regulatory sequences thereof that is responsible for the trait from a suitable source, either by conventional breeding, or genetic modification, in particular by cis-genesis or trans-genesis.
  • Cis-genesis is genetic modification of plants with a natural gene, encoding an (agricultural) trait from the crop plant itself or from a sexually compatible donor plant.
  • Trans-genesis is a genetic modification of a plant with a gene from a non-crossable species or with a synthetic gene.
  • the invention also relates to propagation material suitable for producing a plant which may comprise in its genome a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature.
  • the propagation material is suitable for sexual reproduction.
  • Such propagation material may comprise for example microspores, pollen, ovaries, ovules, embryo sacs and egg cells.
  • the propagation material is suitable for vegetative reproduction.
  • Such propagation material may comprise for example cuttings, roots, stems, cells, protoplasts, and in particular leaves, pollen, embryos, cotyledons, hypocotyls, meristematic cells, root tips, anthers, flowers, seeds and stems.
  • the invention further relates to a plant grown or regenerated from the said propagation material of a plant of the invention, which plant may comprise in its genome a modified NXS gene and/or modified regulatory sequences thereof as defined herein, wherein the modified NXS gene and/or modified regulatory sequences thereof which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature.
  • the invention further relates to a cell of a plant of the invention, which cell may comprise a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature.
  • the cell of the invention is part of a plant or plant part, but the cell may also be in isolated for.
  • the invention also relates to a cell of a plant of the invention, which cell may comprise a modified NXS gene and/or modified regulatory sequences thereof in its genome, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature.
  • the invention also relates to the use of a plant of the invention that may comprise a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature, as a crop.
  • the invention also relates to the use of a plant of the invention that may comprise a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature, as a source of seed.
  • the invention also relates to the use of a plant of the invention that may comprise a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature, as a source of propagating material.
  • the invention also relates to the use of a plant of the invention that may comprise a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature, for consumption.
  • the invention also relates to the use of a plant of the invention that may comprise a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed, provides the seed with the capability to germinate at a high temperature, in plant breeding.
  • the invention further relates to the use of a seed of the invention that may comprise in its genome a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in the seed, provides the seed with the capability to germinate at a high temperature, for sprouting.
  • the term “sprouting” is to mean the practice of germinating a seed for consumption.
  • the invention further relates to the use of a sprouted seed of the invention that may comprise in its genome a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in the seed, provides the seed with the capability to germinate at a high temperature, for consumption.
  • a sprouted seed of the invention may comprise in its genome a modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in the seed, provides the seed with the capability to germinate at a high temperature, for consumption.
  • the term “sprouted seed” is to mean a germinated seed which can be eaten raw or cooked.
  • sprouted seeds that may be eaten raw or cooked may include, but are not limited to the sprouted seeds of the species Rhaphanus sativus, Chenopodium quinoa, Vigna radiata, Medicago sativa, Cicer arietinum, Fagopyrum esculentum, Trigonella foenum - graecum, Allium cepa, Lens esculenta, Phaseolus vulgaris , and Pisum sativum.
  • the invention further relates to a method for producing seeds that are capable of germinating at a high temperature, which may comprise modifying the NXS gene and/or regulatory sequences thereof of the seed to lower the expression level of the gene, to prevent expression of the gene and/or to lower the activity of the encoded NXS protein.
  • modifying the NXS gene and/or regulatory sequences thereof of the seed to lower the expression level of the gene, to prevent expression of the gene and/or to lower the activity of the encoded NXS protein.
  • the modification is achieved by mutating the gene. Mutation is suitably performed on seeds, in particular on seeds that have in their genome a wild type version of the NXS gene.
  • the plant which may comprise the modified NXS gene and/or modified regulatory sequences thereof is a plant of an inbred line, a hybrid, a doubled haploid, or of a segregating population.
  • the invention further provides a method for the production of a plant having the modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed provides the seed with the capability to germinate at a high temperature, by using a doubled haploid generation technique to generate a doubled haploid line which may comprise the high temperature germination trait.
  • the invention furthermore relates to hybrid seed having the modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed provides the seed with the capability to germinate at a high temperature, and to a method for producing such hybrid seed which may comprise crossing a first parent plant with a second parent plant and harvesting the resultant hybrid seed, wherein said first parent plant and said second parent plant is a plant that carries at least one allele of the modified NXS gene and/or modified regulatory sequences thereof.
  • the two parents both have the modified NXS gene and/or modified regulatory sequences thereof they suitably differ in one or more, preferably multiple, other traits.
  • the invention also relates to a method for the production of a plant having the modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed provides the seed with the capability to germinate at a high temperature, by using a seed that may comprise the modified NXS gene and/or modified regulatory sequences thereof for growing the said plant.
  • the invention also relates to a method for seed production which may comprise growing plants from seeds of the invention, allowing the plants to produce seeds, and harvesting those seeds. Production of the seeds is suitably done by crossing or selfing. Preferably, the seeds so produced have the capability to germinate at a high temperature. For this, both parents should have the modified NXS gene and/or modified regulatory sequences thereof.
  • the invention relates to a method for the production of a plant having the modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed provides the seed with the capability to germinate at a high temperature, by using tissue culture.
  • the invention furthermore relates to a method for the production of a plant having the modified NXS gene and/or modified regulatory sequences thereof, which when homozygously present in a seed provides the seed with the capability to germinate at a high temperature, by using vegetative reproduction.
  • the present invention is broadly applicable to all plant species and crops that harbour an NXS gene in their genome. Identification of NXS orthologues, i.e. NXS genes in other species, can be performed in many crops, methods for which are known in the art.
  • BLAST Basic Local Alignment Search Tool
  • FIGS. 1A-C SEQ ID No. 1 and 2
  • Primers were then designed to amplify the complete NXS gene.
  • orthologous NXS protein sequence were identified by Blast X or Blast P as reciprocal best hits to the lettuce NXS or other plant NXS protein sequences.
  • DNA and protein sequences of the NXS orthologues that were identified through this method are represented in FIGS. 2A-2GG , FIGS. 3A-F and Table 1. Multiple sequence alignments of the protein sequences confirmed that these were orthologous NXS genes ( FIGS. 4A-C ).
  • the invention relates to modified versions of the NXS genes and/or modified regulatory sequences thereof of Lactuca sativa, Cichorium endivia, Cichorium intybus, Solanum melongena, Solanum lycopersicum, Capsicum annuum, Capsicum baccatum, Brassica oleracea, Apium graveolens, Spinacia oleracea, Valerianella locusta, Daucus carota, Glycine max, Rhaphanus sativus, Chenopodium quinoa, Vigna radiata, Medicago sativa, Cicer arietinum, Fagopyrum esculentum, Trigonella foenum - graecum, Allium cepa, Lens esculenta, Oryza sativa, Zea mays, Phaseolus
  • the modified NXS gene “when homozygously present” provides seeds with the capability to germinate at a high temperature this is intended to encompass situations in which the modification is recessive but also situations in which the modification is dominant and the high temperature germination capacity is also expressed when the modified gene is present in heterozygous state.
  • Such dominant modifications can be but need not be present in homozygous state but are also visible in heterozygous state. Seeds and plants having such dominant modification and their uses are also part of this invention.
  • NXS orthologues An overview of the NXS orthologues are presented in Table 1. The overview indicates which SEQ ID Nos are linked to which plant species in FIGS. 2A-2GG, 3A -F and 4 A-C. For some plant species, a GI number (GenInfo identifier) and Genbank Accession number is listed, which can be used to retrieve corresponding orthologous NXS sequence.
  • FIGS. 2A-2GG FIGS. 3A-F Zea mays mRNA 670383460 XM_008674309 — — Phaseolus mRNA 593331455 XM_007139092 — vulgaris Citrus sinesis mRNA 572153068 NP_001275861 — — Glycine Max -1 mRNA 571474665 XP_006586290 — — Glycine Max -2 mRNA 571550275 XM_003552678.2 — — Glycine Max -3 Misc_RNA 571554555 XR_137640.2 — — Populus mRNA 566165809 XP_002305164 — — trichocarpa Malus mRNA 372477763 AEX97076 — — domestica Oryza sativa m
  • Seeds of the wild type lettuce varieties Sensa ⁇ and Burovia RZ (both from Rijk Zwaan, De Lier, The Netherlands) were treated with EMS by submergence of approximately 2000 seeds per variety into an aerated solution of either 0.5% (w/v) or 0.7% EMS for 24 hours at room temperature.
  • M2 seeds were harvested and bulked in one pool per variety per treatment. The resulting four pools of M2 seeds were used as starting material to identify the individual M2 seeds containing high temperature germination alleles.
  • the efficacy of the genetic modification procedure was assessed by determining the occurrence of bleached plants, which is indicative for chlorophyll loss due to modification in genes directly or indirectly involved in the formation or accumulation of chlorophyll. Individual plants within each of the 4 pools of M2 seeds were observed to be bleached. This demonstrates that the applied treatments resulted in genetic modifications.
  • Lettuce seeds capable of germinating at a high temperature were identified amongst the M2 seeds that were produced as a result of the EMS treatment described in Example 1.
  • M2 seeds were germinated on wetted filter paper in a closed container.
  • the M2 seeds of Burovia were incubated at 35° C., whilst the M2 seeds of Sensa ⁇ were incubated at 32° C., under continuous dark conditions (24 h/day) in order to mimic natural germination conditions beneath the soil or when seeds are encapsulated in pellets.
  • the confirmed M3 seeds were grown into M3-lines which were then multiplied.
  • Germination tests were performed at different temperatures, to determine the cumulative germination over time at a given temperature for each seed lot of wild type lettuce varieties Sensa ⁇ and Burovia, as well as the EMS treated seeds of the deposit (obtained in Example 2).
  • germination was scored twice a day. A seed was scored as being germinated when radical protrusion through the pericarp of the seed was clearly visible. Germinated seeds were counted and then removed at every counting moment. If there were dead or dormant seeds in the seed lot being tested, germination was followed for at least four extra counting moments until no additional germination was observed. The final germination percentage of a given seed lot, at the given temperature, was determined by plotting a “Germination over Time” curve. The final germination percentage was calculated as the number of germinated seeds at the end of scoring/the number of seeds sown for testing ⁇ 100%.
  • the GT50 Dark was derived per seed lot, by determining the temperature at which the final germination percentage is expected to be 50% (Table 2). When seeds of a given seed lot are exposed to temperatures above the GT50 Dark, they may become thermodormant or die.
  • M2 lettuce plants which yielded M3 seed lots capable of germinating at a high temperature as shown in Examples 3A and 3B, were sequenced. PCR amplification and sequencing primers were designed based on the lettuce ( Lactuca sativa ) NXS DNA sequence according to SEQ ID No. 1.
  • DNA sequencing revealed the presence of a G 3018 >A 3018 mutation (T 3017 G 3018 G 3019 >T 3017 A 3018 G 3018 G 3019 ) in the NXS gene according to SEQ ID No. 1 of Ls_mt_sen, leading to the conversion of a Tryptophan to a premature stop codon at position 140 in the encoded protein according to SEQ ID No. 2.
  • This mutation led to the expression of a truncated, non-functional version of the NXS protein in the M2 plant and corresponding seeds of the M3 seed lot.
  • DNA sequencing revealed the presence of a C 3518 >T 3518 mutation (C 3518 C 3519 A 3520 >T 3518 C 3519 A 3520 ) in the NXS gene according to SEQ ID No. 1, leading to the conversion of a Proline to a Serine at position 212 in the encoded protein according to SEQ ID No. 2.
  • This mutation led to the expression of a non-functional version of the NXS protein in the M2 plant and corresponding seeds of the M3 seed lot.
  • FIGS. 1A-C The DNA and protein sequence of the lettuce NXS gene are shown in FIGS. 1A-C , SEQ ID No. 1 and 2.
  • Orthologues of the NXS gene were identified using a Basic Local Alignment Search Tool (BLAST) to compare the lettuce NXS DNA and protein sequences with the sequences of other plant species. Using this method, 1-2 best hits per species were identified as candidate NXS orthologous genes. Primers were then designed to amplify the complete NXS gene.
  • orthologous NXS protein sequence were identified by Blast X or Blast P as reciprocal best hits to the lettuce NXS or other plant NXS protein sequences.
  • DNA and protein sequences of the NXS orthologues that were identified through this method are represented in FIGS. 2A-2GG , FIGS. 3A-F and Table 1. Multiple sequence alignments of the predicted protein sequences confirmed that these were orthologous NXS genes ( FIGS. 4A-C ).
  • the alignment of the NXS protein of more than 200 unrelated species showed that there are a number of very highly conserved amino acids amongst the NXS orthologues (results not shown).
  • the proline residue at position 212 in the lettuce NXS protein according to SEQ ID No. 2 and encoded by C 3518 C 3519 A 3520 in the lettuce NXS DNA sequence according to SEQ ID No. 1 is part of a highly conserved motif in a number of unrelated species.
  • a non-functional version of the NXS protein as a result of the substitution of the proline residue with a serine residue at this position was found in lettuce mutant Ls_mt_bur (See Example 4). Since the proline at this position is a highly conserved amino acid and/or part of a highly conserved protein motif, its disruption in any of the NXS orthologues would also lead to the production of a non-functional NXS protein.
  • NXS protein of more than 200 unrelated species showed that another very highly conserved amino acid residue amongst the NXS orthologues is a tryptophan residue, which in lettuce is located at position 175 in the lettuce NXS protein according to SEQ ID No. 2 and encoded by T 3196 G 3197 G 3198 in the lettuce NXS DNA sequence according to SEQ ID No. 1.
  • tryptophan is also a highly conserved amino acid and/or part of a highly conserved protein motif, its disruption in any of the NXS orthologues would lead to the production of a non-functional NXS protein.
  • Seeds of the plant species of interest are mutagenized in order to introduce point mutations into the genome. Mutagenesis is achieved using chemical means, such as EMS treatment (see Example 1), or specific targeted means. The skilled person is familiar with both chemical and targeted means for introducing mutations into a genome.
  • Mutagenized seed is then germinated, the resultant plants are selfed or crossed to produce M2 seed.
  • a tilling screen for NXS gene modifications which are responsible for the absence or reduction of NXS gene expression or activity is performed. NXS gene modifications are identified based on the NXS DNA sequences listed in Table 1 for the given plant species. The skilled person is also familiar with tilling (McCallum et. al. (2000) Nature Biotechnology, 18: 455-457) and techniques for identifying nucleotide changes such as DNA sequencing amongst others.
  • Plants with a modified NXS gene are homozygous or made homozygous by selfing, crossing or doubled haploid techniques which are familiar to the skilled person. Seed lots from plants selected on the basis of modifications to the NXS gene are then tested for their ability to germinate at a high temperature. To confirm the high temperature germination trait resulting from modifications of the NXS gene, germination tests in the dark are performed (see Example 3). Seeds belonging to a seed lot having a modified NXS gene and a GT50 Dark which is significantly above the GT50 Dark of the wild type seed lot are identified as plants of the invention.
  • a lettuce plant of the invention grown from seeds of the Burovia NXS mutant Ls_mt_bur which is homozygous for the modification in its NXS gene, was crossed with a wild type lettuce plant, which did not show the trait of the invention.
  • the GT50 Dark of the resulting F1 seeds were determined as described in Examples 3A and 3B.
  • the F1 seeds had the same GT50 Dark as the seeds of the wild type plant (e.g. the seeds are not capable of germinating at a high temperature).
  • a lettuce plant was selected which was selfed to obtain a population of F2 plants.
  • the F2 plants were again selfed to produce F3 seed lots.
  • These F3 seed lots were then germinated in the dark at 35° C. In approximately one quarter of the F3 seed lots, of the seeds tested no seeds germinated. In approximately another quarter of the F3 seed lots, nearly 100% of the seeds tested germinated, which indicated that the mutated NXS allele was present in the corresponding F2 mother plant in a homozygous state.
  • An F3 plant was then grown from an F3 seed lot which had the modified NXS gene homozygously present in the corresponding F2 mother plant. This F3 plant was used for further crossing to transfer the trait of the invention to other lettuce plants.
  • the trait of the invention can be transferred from a plant of any one of the species listed in Table 1 which carries a modified orthologous NXS gene, into a corresponding wild type plant that does not exhibit the trait of the invention.
  • F2 plants and later generations need to be selfed or crossed in order to produce seed.
  • the skilled person is familiar with the selfing and crossing steps necessary for a given plant species.
  • the segregation ratio of the trait of the invention for a given plant species is also dependent on the number of orthologous copies of the NXS gene present that is present in the genome of the species. Regardless, the segregation of the trait of the invention should still correspond to a monogenic recessive inheritance.
  • a seed comprising in its genome a modified NXS gene and/or modified regulatory sequences thereof.
  • a plant comprising in its genome a modified NXS gene and/or modified regulatory sequences thereof, wherein the modified NXS gene is as defined in any one of the paragraphs 2 to 7.
  • a lettuce seed ( Lactuca sativa ) comprising in its genome a modified NXS gene, the wild type of which is identified in SEQ ID No. 1, encoding the protein of SEQ ID No.2.
  • the seed lot of paragraph 25, wherein the GT50 Dark of the seed lot of seeds comprising a modified NXS gene is between 10° C. and 25° C., between 11° C. and 25° C., between 12° C. and 25° C., between 13° C. and 25° C., between 14° C. and 25° C., between 15° C. and 25° C., between 16° C. and 25° C., between 17° C. and 25° C., between 18° C. and 25° C., between 19° C. and 25° C., between 20° C. and 25° C., between 21° C. and 25° C., between 22° C. and 25° C., between 23° C. and 25° C. and between 24° C. and 25° C. higher than the GT50 Dark of a seed lot of seeds which do not comprise the modified NXS gene.
  • a lettuce plant comprising in its genome a modified NXS gene as defined in any one of the paragraphs 15 to 24.
  • Propagation material of paragraph 33 wherein the propagation material is selected from the group consisting of microspores, pollen, ovaries, ovules, embryos, embryo sacs, egg cells, cuttings, roots, root tips, hypocotyls, cotyledons, stems, leaves, flowers, anthers, seeds, meristematic cells, protoplasts, and cells.
  • a modified Lactuca sativa NXS gene the wild type of which is identified in SEQ ID No. 1, encoding the protein of SEQ ID No. 2, and wherein the modified gene is as defined in any one of the paragraphs 15 to 24.

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